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- PDB-6liy: SeMet CRL Protein of Arabidopsis -

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Basic information

Entry
Database: PDB / ID: 6liy
TitleSeMet CRL Protein of Arabidopsis
ComponentsChromophore lyase CRL, chloroplastic
KeywordsLYASE / a homolog of cyanobacterial CpcT lyase / PLANT PROTEIN
Function / homology
Function and homology information


transport of virus in host, tissue to tissue / plastid fission / protein-phycocyanobilin linkage / chloroplast outer membrane / Lyases / chloroplast fission / plastid / regulation of cell division / response to reactive oxygen species / cellular response to virus ...transport of virus in host, tissue to tissue / plastid fission / protein-phycocyanobilin linkage / chloroplast outer membrane / Lyases / chloroplast fission / plastid / regulation of cell division / response to reactive oxygen species / cellular response to virus / defense response / lyase activity / cell cycle / cell division
Similarity search - Function
Chromophore lyase CpcT/CpeT / Chromophore lyase CpcT/CpeT superfamily / CpeT/CpcT family (DUF1001)
Similarity search - Domain/homology
Chromophore lyase CRL, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.761 Å
AuthorsWang, F.F. / Guan, K.L. / Sun, P.K. / Xing, W.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Plant J. / Year: 2020
Title: The Arabidopsis CRUMPLED LEAF protein, a homolog of the cyanobacterial bilin lyase, retains the bilin-binding pocket for a yet unknown function.
Authors: Wang, F. / Fang, J. / Guan, K. / Luo, S. / Dogra, V. / Li, B. / Ma, D. / Zhao, X. / Lee, K.P. / Sun, P. / Xin, J. / Liu, T. / Xing, W. / Kim, C.
History
DepositionDec 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromophore lyase CRL, chloroplastic
B: Chromophore lyase CRL, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5044
Polymers61,1132
Non-polymers3902
Water5,116284
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint13 kcal/mol
Surface area18680 Å2
Unit cell
Length a, b, c (Å)38.289, 73.540, 67.147
Angle α, β, γ (deg.)90.000, 97.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chromophore lyase CRL, chloroplastic / Protein CONSTITUTIVE ACTIVATOR OF AAA-ATPase 33 / Protein CRUMPLED LEAF


Mass: 30556.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CRL, CAA33, At5g51020, K3K7.20 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9FI46, Lyases
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1 M MES pH 6.5, 12% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 35639 / % possible obs: 97.2 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.033 / Rrim(I) all: 0.089 / Χ2: 3.159 / Net I/σ(I): 13.4 / Num. measured all: 267556
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.76-1.797.40.82517530.8450.3240.8881.25496
1.79-1.827.70.6917720.9030.2650.7391.31495.7
1.82-1.867.80.57217230.930.2190.6131.31796.4
1.86-1.97.80.48117770.9440.1840.5151.42596.7
1.9-1.947.80.36117500.9650.1390.3871.54496.5
1.94-1.987.80.28317670.9810.1090.3031.64196.3
1.98-2.037.70.24417990.980.0940.2621.71996.8
2.03-2.097.70.20517240.9840.0790.221.84897.1
2.09-2.157.70.17617880.990.0680.1891.99797.3
2.15-2.227.70.15417800.9910.0590.1652.15797.1
2.22-2.37.70.1417710.9920.0540.152.44897.5
2.3-2.397.70.12718000.9930.0490.1362.63597.5
2.39-2.57.60.11117680.9940.0430.1192.92697.6
2.5-2.637.60.118000.9950.0390.1073.36498
2.63-2.797.50.09718070.9940.0380.1044.07598
2.79-3.017.30.0818010.9960.0320.0864.65798.5
3.01-3.317.20.07118190.9960.0290.0765.6398.3
3.31-3.7970.06318110.9960.0260.0686.18998.2
3.79-4.786.80.05618210.9970.0230.0616.52398.1
4.78-506.80.06618080.9960.0270.07210.16295.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.761→32.193 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 1841 5.17 %
Rwork0.2069 33755 -
obs0.2088 35596 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.47 Å2 / Biso mean: 32.8181 Å2 / Biso min: 16.29 Å2
Refinement stepCycle: final / Resolution: 1.761→32.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 24 284 3412
Biso mean--36.02 37.2 -
Num. residues----391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.761-1.80820.32941280.2681255896
1.8082-1.86140.35721400.2645255296
1.8614-1.92150.24351320.2426260196
1.9215-1.99010.26721430.2262253397
1.9901-2.06980.25911460.2328257997
2.0698-2.1640.24081380.2267259597
2.164-2.2780.29041450.2299258498
2.278-2.42070.27951450.2282260097
2.4207-2.60750.2781580.2319259698
2.6075-2.86980.27211360.227262698
2.8698-3.28470.23041500.2037261898
3.2847-4.1370.21811320.1823267898
4.137-32.1930.21231480.1803263597

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